Late-onset hypogonadism (LOH) is a clinical and biochemical syndrome associated with age and featured by typical symptoms and reduced blood testosterone level. Among males aged over 30 years, the incidence of androgen deficiency is 7 to 30%. The aim of this study was to investigate the incidence of hypogonadism in patients aged over 40 years with an underlying condition and/or a comorbidity, such as arterial hypertension, Chronic obstructive pulmonary disease (COPD), metabolic syndrome, Type 2 of diabetes mellitus, dyslipidaemia, adiposity in various General practice (GP) and physician-sexologists’ offices in Latvia, and to determine the influence of chronic diseases on the development of hypogonadism. Males aged 39 years who turned to family doctors at nine GP were offered to fill in Aging Male Study (AMS) questionnaires used for the diagnostics of late-onset hypogonadism. Males aged 40 years who visited the office of the physician sexologist Anatolijs Požarskis were offered to fill in the same questionnaires. After compiling the data from AMS questionnaires, a group of males exhibiting signs of LOH were isolated (in total 1222 persons). In these patients, we determined blood testosterone and sex-hormone binding globulin (SHBG) levels. Chronic diseases were found in these men in data evaluation of patient medical records, and after performing physical and laboratory examinations. Late-onset hypogonadism was laboratory-diagnosed in 79% of patients with signs of late-onset hypogonadism in accordance with the AMS questionnaires and with concomitant diseases and in 4.7% of patients with signs of late-onset hypogonadism in accordance with the AMS questionnaires and without the aforementioned concomitant diseases. Persons with arterial hypertension, dyslipidaemia, adiposity, metabolic syndrome, COPD and Type 2 of diabetes mellitus had higher chance of developing hypogonadism (p < 0.001). Arterial hypertension, dyslipidaemia, adiposity, metabolic syndrome, COPD statistically significantly (p < 0.001) decreased the level of total testosterone by 0.47, 1.18, 0.36, 0.67, and 0.18 ng/ml, respectively, and decreased the level of free testosterone by 2.52, 2.71, 1,69, 6.77, and 4.58 pg/ml, respectively. Type 2 diabetes mellitus had no statistically significant effect on the level of total and free testosterone (p = 0.95, p = 0.10). The most significant decrease in the level of testosterone was observed in cases of dyslipidemia, COPD and metabolic syndrome. General physicians should pay special attention to patients with this disease, as these patients belong to a group with a high risk of development of expressed LOH syndrome.